biomaRt: refseq gene details
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.7 years ago
Hi, I was trying to get the gene details of refseq ids (these are output from blastn) with the following code: =================   library(biomaRt)   mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")   attr <- c("refseq_mrna",'hgnc_symbol', 'chromosome_name','start_position','end_position')   ids <- c("NM_001270493", "NM_001185076","NM_001185075","NM_001185082")   xx <- getBM(attributes=attr,               filters = "refseq_mrna", values = ids, mart = mart)   print(xx) =============== The results are: >   print(xx)    refseq_mrna hgnc_symbol chromosome_name start_position end_position 1 NM_001185075        FMR1               X      146993469    147032645 2 NM_001185076        FMR1               X      146993469    147032645 How can I get details of the other two refseq ids that do not show up in the results? thanks! Tim [[alternative HTML version deleted]]
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@steffen-durinck-4465
Last seen 7.7 years ago
Hi Tim, By default getBM queries go to the central BioMart service, they are lagging a bit behind with the Ensembl version that they host and are running v69. If you do your query on the latest version of Ensembl you get results for one more of your ids: mart <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host="www.ensembl.org") attr <- c("refseq_mrna",'hgnc_symbol', 'chromosome_name','start_position','end_position') ids <- c("NM_001270493", "NM_001185076","NM_001185075","NM_001185082") xx <- getBM(attributes=attr,filters = "refseq_mrna", values = ids, mart = mart) > xx refseq_mrna hgnc_symbol chromosome_name start_position end_position 1 NM_001185075 FMR1 X 146993469 147032645 2 NM_001185076 FMR1 X 146993469 147032645 3 NM_001185082 FMR1 X 146993469 147032645 The missing id NM_001270493 might be to novel to have been included in the latest Ensembl build. To find out for sure you could email the Ensembl helpdesk at helpdesk@ensembl,org Cheers, Steffen On Fri, May 24, 2013 at 4:46 AM, Tim Smith <tim_smith_666@yahoo.com> wrote: > Hi, > > I was trying to get the gene details of refseq ids (these are output from > blastn) with the following code: > > ================= > > library(biomaRt) > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > attr <- c("refseq_mrna",'hgnc_symbol', > 'chromosome_name','start_position','end_position') > ids <- c("NM_001270493", "NM_001185076","NM_001185075","NM_001185082") > > xx <- getBM(attributes=attr, > filters = "refseq_mrna", values = ids, mart = mart) > > print(xx) > =============== > > The results are: > > print(xx) > refseq_mrna hgnc_symbol chromosome_name start_position end_position > 1 NM_001185075 FMR1 X 146993469 147032645 > 2 NM_001185076 FMR1 X 146993469 147032645 > > > How can I get details of the other two refseq ids that do not show up in > the results? > > > thanks! > > Tim > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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